[BioC] GC counts

[Devon Ryan]

FYI, this ended up getting discussed on biostars (http://www.biostars.org/p/82308/) and the context turned out to be RNAseq normalization (the question ended up being answered there as well).

____________________________________________
Devon Ryan, Ph.D.
Email: dpryan at dpryan.com
Tel: +49 (0)178 298-6067
Molecular and Cellular Cognition Lab
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn, Germany

On Sep 30, 2013, at 5:19 PM, Steve Lianoglou wrote:

> Hi Catarina,
> 
> On Sat, Sep 28, 2013 at 3:59 AM, Catarina [guest]
> <guest at bioconductor.org> wrote:
>> 
>> Hi!
>> 
>> I'm very new to genetic and I'm afraid I have the most basic question. Why do you normalize for GC counts and not for AT counts? I know that GC establishes 3 hydrogen bounds and AT only two. The stronger the bound, the easier to determine where it is/how many there are? Is this ti?
> 
> Can you be more specific? Can you provide the context of the
> normalization you are talking about? I mean, is there a particular
> assay you are working with (PCR? next gen seq? microarray?) that
> you've found a "normalization" required for GC content?
> 
> You will find a lot of (general and specific) information on this
> topic if you simply google for "gc bias".
> 
> If that is not sufficient, please ask a more specific question as it
> relates to the (bioinformatics) problem you are  trying to solve.
> 
> HTH,
> 
> -steve
> 
> -- 
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
> 
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